BondStereoFlagCalculator.hpp

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/* 
 * BondStereoFlagCalculator.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_CHEM_BONDSTEREOFLAGCALCULATOR_HPP
#define CDPL_CHEM_BONDSTEREOFLAGCALCULATOR_HPP
 
#include <cstddef>
#include <vector>
#include <utility>
#include <memory>
#include <functional>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Math/VectorArray.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Atom;
        class Bond;
 
        class CDPL_CHEM_API BondStereoFlagCalculator
        {
 
          public:
            typedef std::function<const Math::Vector2D&(const Atom&)> Atom2DCoordinatesFunction;
 
            BondStereoFlagCalculator();
 
            BondStereoFlagCalculator(const MolecularGraph& molgraph, Util::UIArray& flags);
 
            BondStereoFlagCalculator(const BondStereoFlagCalculator&) = delete;
 
            BondStereoFlagCalculator& operator=(const BondStereoFlagCalculator&) = delete;
 
            void setAtom2DCoordinatesFunction(const Atom2DCoordinatesFunction& func);
 
            const Atom2DCoordinatesFunction& getAtom2DCoordinatesFunction() const;
 
            void calculate(const MolecularGraph& molgraph, Util::UIArray& flags);
 
          private:
            class StereoAtomInfo;
 
            void init(const MolecularGraph&, Util::UIArray&);
 
            void assignStereoFlags(Util::UIArray&);
 
            void assignFlagsForEitherDoubleBonds(Util::UIArray&);
            void assignFlagsForIsolatedCenter(const StereoAtomInfo*, Util::UIArray&);
            bool assignFlagsForNonIsolatedCenters(std::size_t, std::size_t, Util::UIArray&);
 
            void switchStereoFlag(std::size_t);
 
            class StereoAtomInfo
            {
 
              public:
                typedef std::shared_ptr<StereoAtomInfo> SharedPointer;
 
                StereoAtomInfo(const MolecularGraph*, const Atom2DCoordinatesFunction& coords_func,
                               const Atom*, unsigned int, std::size_t, const Atom**, const Bond**);
 
                unsigned int getConfiguration() const;
 
                void findBestBondOrder(const Util::BitSet&, const Util::BitSet&);
 
                bool hasStereoAtomNbrs() const;
 
                bool configMatches(const Util::UIArray&) const;
 
                std::size_t getNumBonds() const;
 
                std::size_t getBondIndex(std::size_t) const;
                std::size_t getNbrAtomIndex(std::size_t) const;
 
                std::size_t getAtomIndex() const;
 
              private:
                typedef std::pair<const Atom*, std::size_t> Ligand;
 
                const MolecularGraph* molGraph;
                const Atom*           atom;
                unsigned int          configuration;
                std::size_t           numBonds;
                bool                  hasStereoNbrs;
                double                configCalcTerms[4];
                bool                  bondEndFlags[4];
                Ligand                ligands[4];
                Ligand                orderedLigands[4];
            };
 
            typedef std::vector<StereoAtomInfo*>               StereoAtomInfoList;
            typedef std::vector<StereoAtomInfo::SharedPointer> StereoAtomInfoPtrTable;
            typedef std::vector<const Bond*>                   BondList;
 
            const MolecularGraph*     molGraph;
            Atom2DCoordinatesFunction coordsFunc;
            Util::UIArray             currentStereoFlags;
            StereoAtomInfoPtrTable    stereoAtomTable;
            StereoAtomInfoList        stereoAtomList;
            BondList                  eitherBondList;
            Util::BitSet              stereoAtomMask;
            Util::BitSet              configMatchMask;
            Util::BitSet              stereoDBAtomMask;
            Util::BitSet              ringBondMask;
            Util::BitSet              singleBondMask;
            std::size_t               numMismatchingCtrs;
            std::size_t               minNumMismatchingCtrs;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_BONDSTEREOFLAGCALCULATOR_HPP